So let me see if I understand this. Microsoft went through all the trouble of implementing a new licensing scheme to earn
less money?

No.

Microsoft wrote:

Instead of licensing every inactive or stored virtual instance of a Windows Server System product, customers can now create and store an unlimited number of instances, including those for back-up and recovery, and only pay for the maximum number of running
instances at any given time.

Microsoft wrote:

Therefore, we now have a policy for Windows Server 2003 R2 Enterprise Edition that allows customers to run up to four running virtual instances on one server at no additional cost. And we’ll go further with the Datacenter Edition of Windows Server "Longhorn,"
the code name for the next version of Windows Server, by allowing customers to run unlimited virtual instances on one server at no additional charge.

If you want to see what analysts are saying about this, instead of random slashdot commenters , here's an interesting article from eWeek:

Microsoft Corp. customers reacted with surprise and even some disbelief Monday at the software giant's announcement that it was simplifying its software licensing terms for virtual machine environments.
...
Microsoft customers who attended the briefing Monday questioned Kelly on why the company would implement a licensing policy that would have the potential of sharply cutting its server licensing revenue.

It doesn't go into the previous lead we've taken in similar areas - iirc we decided not to charge extra SQL Server licensing fees when hyperthreading/multicore CPUs appeared, and then IBM and Oracle had to play catch up. Looks like that's going to happen
all over:

"I think other vendors are going to have to sit down and immediately start making adjustments," Lewis said.
"But they aren't necessarily going to do it happily, because it is far different from what they are used to doing," she said.